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公开(公告)号：US12062418B2
公开(公告)日：2024-08-13
申请号：US18165133
申请日：2023-02-06
申请人： 10X Genomics, Inc.
发明人： Jeffrey Mellen , Kevin J. Wu , Vijay Kumar Sreenivasa Gopalan , Nicolaus Lance Hepler , Jasper Staab
摘要： A dataset is obtained comprising data blocks, each representing a different characteristic, for a plurality of cells across a plurality of bins, each bin representing a different portion of a reference sequence. Cells are clustered on one such characteristic across the bins thereby forming a tree that includes root, intermediate, and terminal nodes, where the cells are terminal nodes and intermediate nodes have daughter nodes, themselves being intermediate nodes or a cell. A subset of the tree is displayed that includes the root and leaves, each leaf representing an intermediate node or a cell. A heat map of the characteristic is also displayed, the map including a segment for each leaf, across the bins. When a segment represents an intermediate node, it is an average of the characteristic across daughters of the node. Graphs of characteristics for the root across the bins are also displayed.
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公开(公告)号：US20200005902A1
公开(公告)日：2020-01-02
申请号：US16454485
申请日：2019-06-27
申请人： 10X Genomics, Inc.
发明人： Jeffrey Mellen , Kevin J. Wu , Vijay Kumar Sreenivasa Gopalan , Nicolaus Lance Hepler , Jasper Staab
摘要： A dataset is obtained comprising data blocks, each representing a different characteristic, for a plurality of cells across a plurality of bins, each bin representing a different portion of a reference sequence. Cells are clustered on one such characteristic across the bins thereby forming a tree that includes root, intermediate, and terminal nodes, where the cells are terminal nodes and intermediate nodes have daughter nodes, themselves being intermediate nodes or a cell. A subset of the tree is displayed that includes the root and leaves, each leaf representing an intermediate node or a cell. A heat map of the characteristic is also displayed, the map including a segment for each leaf, across the bins. When a segment represents an intermediate node, it is an average of the characteristic across daughters of the node. Graphs of characteristics for the root across the bins are also displayed.
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公开(公告)号：US20240218445A1
公开(公告)日：2024-07-04
申请号：US18406946
申请日：2024-01-08
申请人： 10X Genomics, Inc.
发明人： Alexander Y. Wong , Jeffrey Mellen , Kevin Wu , Paul Ryvkin
IPC分类号： C12Q1/6881 , C07K14/725 , C07K16/28 , G16B30/00 , G16B40/30 , G16B45/00 , C12Q1/6806 , C12Q1/686 , C12Q1/6883 , G16B30/10
CPC分类号： C12Q1/6881 , C07K14/7051 , C07K16/2809 , G16B30/00 , G16B40/30 , G16B45/00 , C07K2317/565 , C12Q1/6806 , C12Q1/686 , C12Q1/6883 , C12Q2600/156 , C12Q2600/158 , C12Q2600/16 , G16B30/10
摘要： Methods for screening clonotypes are provided. Data representing a plurality of cells from a single subject is obtained. The data represents a plurality of clonotypes. The data includes a plurality of contigs for each respective clonotype in the plurality of clonotypes. Each respective contig in the plurality of contigs comprises (i) an indication of chain type for the respective contig and (ii) a contig sequence of an mRNA of the respective cell. There is determined, using the data, for each respective clonotype in the plurality of clonotypes, a number of the plurality of cells that represent the respective clonotype. In some instances, more than one cell in the plurality of cells have the same clonotype in the plurality of clonotypes. In some instances, the plurality of clonotypes comprises 25 clonotypes and where the plurality of cells includes at least one cell for each clonotype in the plurality of clonotypes.
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公开(公告)号：US20180225416A1
公开(公告)日：2018-08-09
申请号：US15891607
申请日：2018-02-08
申请人： 10X Genomics, Inc.
发明人： Alexander Y. Wong , Jeffrey Mellen , Kevin Wu , Paul Ryvkin
摘要： A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity in a plurality of first entities for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters. Differences in the discrete attribute values for the first entity across the second entities of a given cluster relative to the discrete attribute value for the same first entity across the other clusters are computed thereby deriving differential values. A heat map of these differential values for each first entity for each cluster is displayed to reveal the pattern in the dataset.
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公开(公告)号：US11954614B2
公开(公告)日：2024-04-09
申请号：US16442800
申请日：2019-06-17
申请人： 10X Genomics, Inc.
发明人： Alexander Y. Wong , Jeffrey Mellen , Kevin J. Wu , Paul Ryvkin , Preyas Shah , Patrick Marks , Niranjan Srinivas
CPC分类号： G06N7/01 , G06F16/285 , G06F16/904 , G16B25/10 , G16B40/00 , G16B45/00 , G16B50/30
摘要： A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity of a first type in a plurality of first entities of the first type and discrete attribute values for each first entity of a second type in a plurality of first entities of the second type for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters.
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公开(公告)号：US20230368869A1
公开(公告)日：2023-11-16
申请号：US18165133
申请日：2023-02-06
申请人： 10X Genomics, Inc.
发明人： Jeffrey Mellen , Kevin J. Wu , Vijay Kumar Sreenivasa Gopalan , Nicolaus Lance Hepler , Jasper Staab
摘要： A dataset is obtained comprising data blocks, each representing a different characteristic, for a plurality of cells across a plurality of bins, each bin representing a different portion of a reference sequence. Cells are clustered on one such characteristic across the bins thereby forming a tree that includes root, intermediate, and terminal nodes, where the cells are terminal nodes and intermediate nodes have daughter nodes, themselves being intermediate nodes or a cell. A subset of the tree is displayed that includes the root and leaves, each leaf representing an intermediate node or a cell. A heat map of the characteristic is also displayed, the map including a segment for each leaf, across the bins. When a segment represents an intermediate node, it is an average of the characteristic across daughters of the node. Graphs of characteristics for the root across the bins are also displayed.
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公开(公告)号：US20240354607A1
公开(公告)日：2024-10-24
申请号：US18629826
申请日：2024-04-08
申请人： 10X Genomics, Inc.
发明人： Alexander Y. Wong , Jeffrey Mellen , Kevin J. Wu , Paul Ryvkin , Preyas Shah , Patrick Marks , Niranjan Srinivas
CPC分类号： G06N7/01 , G06F16/285 , G06F16/904 , G16B25/10 , G16B40/00 , G16B45/00 , G16B50/30
摘要： A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity of a first type in a plurality of first entities of the first type and discrete attribute values for each first entity of a second type in a plurality of first entities of the second type for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters.
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公开(公告)号：US11898206B2
公开(公告)日：2024-02-13
申请号：US15984324
申请日：2018-05-19
申请人： 10X Genomics, Inc.
发明人： Alexander Y. Wong , Jeffrey Mellen , Kevin Wu , Paul Ryvkin
IPC分类号： C07K14/725 , G16B45/00 , G16B40/30 , G16B30/00 , C12Q1/686 , G16B30/10 , C12Q1/6881 , C07K16/28 , C12Q1/6883 , C12Q1/6806
CPC分类号： C12Q1/6881 , C07K14/7051 , C07K16/2809 , G16B30/00 , G16B40/30 , G16B45/00 , C07K2317/565 , C12Q1/686 , C12Q1/6806 , C12Q1/6883 , C12Q2600/156 , C12Q2600/158 , C12Q2600/16 , G16B30/10
摘要： Methods for screening clonotypes are provided. Data representing a plurality of cells from a single subject is obtained. The data represents a plurality of clonotypes. The data includes a plurality of contigs for each respective clonotype in the plurality of clonotypes. Each respective contig in the plurality of contigs comprises (i) an indication of chain type for the respective contig and (ii) a contig sequence of an mRNA of the respective cell. There is determined, using the data, for each respective clonotype in the plurality of clonotypes, a number of the plurality of cells that represent the respective clonotype. In some instances, more than one cell in the plurality of cells have the same clonotype in the plurality of clonotypes. In some instances, the plurality of clonotypes comprises 25 clonotypes and where the plurality of cells includes at least one cell for each clonotype in the plurality of clonotypes.
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公开(公告)号：US11574706B2
公开(公告)日：2023-02-07
申请号：US16454485
申请日：2019-06-27
申请人： 10X Genomics, Inc.
发明人： Jeffrey Mellen , Kevin J. Wu , Vijay Kumar Sreenivasa Gopalan , Nicolaus Lance Hepler , Jasper Staab
摘要： A dataset is obtained comprising data blocks, each representing a different characteristic, for a plurality of cells across a plurality of bins, each bin representing a different portion of a reference sequence. Cells are clustered on one such characteristic across the bins thereby forming a tree that includes root, intermediate, and terminal nodes, where the cells are terminal nodes and intermediate nodes have daughter nodes, themselves being intermediate nodes or a cell. A subset of the tree is displayed that includes the root and leaves, each leaf representing an intermediate node or a cell. A heat map of the characteristic is also displayed, the map including a segment for each leaf, across the bins. When a segment represents an intermediate node, it is an average of the characteristic across daughters of the node. Graphs of characteristics for the root across the bins are also displayed.
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公开(公告)号：US20190332963A1
公开(公告)日：2019-10-31
申请号：US16442800
申请日：2019-06-17
申请人： 10X Genomics, Inc.
发明人： Alexander Y. Wong , Jeffrey Mellen , Kevin J. Wu , Paul Ryvkin , Preyas Shah , Patrick Marks , Niranjan Srinivas
IPC分类号： G06N7/00 , G06F16/28 , G06F16/904
摘要： A visualization system comprising a persistent memory, storing a dataset, and a non-persistent memory implements a pattern visualizing method. The dataset contains discrete attribute values for each first entity of a first type in a plurality of first entities of the first type and discrete attribute values for each first entity of a second type in a plurality of first entities of the second type for each second entity in a plurality of second entities. The dataset is compressed by blocked compression and represents discrete attribute values in both compressed sparse row and column formats. The discrete attribute values are clustered to assign each second entity to a cluster in a plurality of clusters.
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